Since some time we are observing strange things happening to using files from
our local data libraries in our local galaxy-central instance:
The files and hierarchy stay there but when copied to the history. they
turn up as being deleted and can only be used by selecting the view_deleted
Lance Parsons wrote:
I'm running a local instance of Galaxy that has been working quite
well. However, I've recently run into a problem when importing
datasets from a data library into a history. The Size on Disk of
the history grows by the size of the imported dataset, however, the
new
Bossers, Alex wrote:
Since some time we are observing strange things happening to using files from
our local data libraries in our local galaxy-central instance:
The files and hierarchy stay there but when copied to the history. they
turn up as being deleted and can only be used by
Jean-Baptiste Denis wrote:
Hello evyerbody,
i guess this question has already been answered, but i didn't find any :/
Is there a way to reload a tool file from the command line ? I'd
like to automate the process when a user upload a new version of an
existing tool. Am I reinventing the
Hi Nate,
Thanks for this! It has saved me wasting time barking up an inappropriate tree,
and we'll rethink the plans.
Regards,
Mike.
--
Mike Wallis +44(0)113 343 1880
ARC/HPC Systems Support
ISS, University of Leeds, Leeds, LS2 9JT, UK
-Original Message-
From: Nate Coraor
Good catch, that does indeed seem to be the issue. And it only seems to
happen with my older data libraries.
I didn't see a bug report for this, but I'd be happy to file one and/or
take a stab at a fix if someone can point me in the right direction in
the code.
Lance
Nate Coraor wrote:
There are several files in Datatypes with doctest tests in them. Is there a
convenient wrapper script to run them all?
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.commailto:jdu...@illumina.com
Hi John,
You can do: sh run_unit_tests.sh to run these, along with the other doctests
in the core code.
Thanks for using Galaxy,
Dan
On Oct 5, 2011, at 1:17 PM, Duddy, John wrote:
There are several files in Datatypes with doctest tests in them. Is there a
convenient wrapper script to run
Ah, sorry, I just saw your note to Alex regarding the pieces of code to
check out. I'll start doing some digging and let you know if I find
anything out.
See line 1925 in lib/galaxy/web/controllers/library_common.py. Try
adding a bit of debugging to find out if hda.deleted == True when the
Lance Parsons wrote:
Good catch, that does indeed seem to be the issue. And it only
seems to happen with my older data libraries.
I didn't see a bug report for this, but I'd be happy to file one
and/or take a stab at a fix if someone can point me in the right
direction in the code.
Any
Can we introduce new file types via tools in the tool shed? It seems Galaxy can
load them if they are in the datatypes configuration file. Does tool
installation automate the editing of that file?
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Hi,
We have a local galaxy instance running on mac osx connected to a mysql
database. We are having an issue downloading files which are 2Gb. I've
read posts on this mailing list that mention that there is a browser limit
on downloading files of this size, which is fine -- a command-line method
On Oct 5, 2011, at 2:25 PM, Roy Weckiewicz wrote:
Hi,
We have a local galaxy instance running on mac osx connected to a mysql
database. We are having an issue downloading files which are 2Gb. I've read
posts on this mailing list that mention that there is a browser limit on
Hi Roy,
Have you tried setting debug=False and use_interactive=False in the
universe_wsgi.ini file?
Thanks for using Galaxy,
Dan
On Oct 5, 2011, at 2:32 PM, Glen Beane wrote:
On Oct 5, 2011, at 2:25 PM, Roy Weckiewicz wrote:
Hi,
We have a local galaxy instance running on mac osx
Nate Coraor wrote:
michael burrell (TOC) wrote:
Good afternoon all,
I am having some issues with hg performing an update, it wants to use
vimdiff and this is not the way I like to work. According to the mercurial
simply placing the folloing in the ~/.hgrc should make mercurial
I have been having trouble getting cufflinks to run with the -g or -G
parameters via Galaxy. when I select either use reference annotation or use
reference annotation as guide from the pulldown menu, cufflinks runs , but
the -g or -G is not added to the cufflinks command. I think I have
Curt,
You are correct, this is a bug. It was fixed in this changeset:
https://bitbucket.org/galaxy/galaxy-central/changeset/ff7c8c0bef60
We'll be updating galaxy-dist in the next week and this change will be
available then.
Thanks,
J.
On Oct 5, 2011, at 5:54 PM, Curt Palm wrote:
I have
I believe I may have found the bug...
Line 258 of cleanup_datasets.py is the query for library_dataset_ids
when force_retry is set. While it correctly eliminates the the
app.model.LibraryDataset.table.c.purged == False from the where clause,
it incorrectly eliminates the
Hello John,
The Galaxy tool shed currently is not enabled to automatically edit the
datatypes_conf.xml file, although I could add this feature if the need exists.
Can you elaborate on what you are looking to do regarding this?
Thanks!
On Oct 5, 2011, at 1:52 PM, Duddy, John wrote:
Can we
One of the things we're facing is the sheer size of a whole human genome at 30x
coverage. An effective way to deal with that is by compressing the FASTQ files.
That works for BWA and our ELAND, which can directly read a compressed FASTQ,
but other tools crash when reading compressed FASTQ
Hi,
I noticed on that on the manage users page, even after deleting and
purging users (by clicking on the delete and purge buttons on that page),
their account still sticks around in the db. How does one remove these
accounts permanently? Is there a script to do this?
Thanks,
Len
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